fix the bug in CalibratedYule #497

LinguaPhylo · Aug 14, 2024 · 70a5157 · 70a5157
1 parent 148e0dd
commit 70a5157
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diff --git a/lphy-base/src/main/java/lphy/base/evolution/birthdeath/CalibratedYule.java b/lphy-base/src/main/java/lphy/base/evolution/birthdeath/CalibratedYule.java
@@ -201,9 +201,9 @@ private void coalesce(double lambda, double t) {
                     // if there is only one node in activeNodes and is not from inactiveNodes
                     // then add the youngest node from inactiveNodes to activeNodes
                     if (activeNodes.size() == 1 && !activeNodes.contains(getYoungestNode(inactiveNodes))) {
+                        t = getYoungestNode(inactiveNodes).getAge();
                         activeNodes.add(getYoungestNode(inactiveNodes));
                         inactiveNodes.remove(getYoungestNode(inactiveNodes));
-                        t = getYoungestNode(inactiveNodes).getAge();
                     }
                 }
             } else coalesceNodes(activeNodes, t);

diff --git a/lphy-base/src/test/java/lphy/base/evolution/tree/CalibratedYuleTest.java b/lphy-base/src/test/java/lphy/base/evolution/tree/CalibratedYuleTest.java
@@ -109,4 +109,28 @@ void test3() { // test same clade names
         assert observe.getRoot().getAllLeafNodes().stream().anyMatch(node -> node.getId().equals("clade1_taxa3"));
         assert observe.getRoot().getAllLeafNodes().stream().anyMatch(node -> node.getId().equals("clade0_taxa10"));
     }
+
+    @Test
+    void coalesceTest() {
+        double birthRate = 0.1;
+        int n = 20;
+        String[] taxa = {"1", "2", "3", "4", "5", "6", "7", "8", "9", "10"};
+        Number[] cladeAge = new Number[]{29};
+
+        Value<Number> birthRateValue = new Value<>("birthRate", birthRate);
+        Value<Integer> nValue = new Value<>("n", n);
+        Value taxaValue = new Value("taxa", taxa);
+        Value<Number[]> cladeAgeValue = new Value<>("cladeAge", cladeAge);
+        Value<Number> rootAgeValue = new Value<>("rootAge", 31);
+
+        CalibratedYule instance = new CalibratedYule(birthRateValue, nValue, taxaValue, cladeAgeValue, null, rootAgeValue);
+        TimeTree observe = instance.sample().value();
+
+        // node number should be same
+        assertEquals(n , observe.getRoot().getAllLeafNodes().size());
+        // randomly check the names for clade taxa
+        assert observe.getRoot().getAllLeafNodes().stream().anyMatch(node -> node.getId().equals("clade_1"));
+        assert observe.getRoot().getAllLeafNodes().stream().anyMatch(node -> node.getId().equals("clade_3"));
+        assert observe.getRoot().getAllLeafNodes().stream().anyMatch(node -> node.getId().equals("clade_10"));
+    }
 }